Fgd2 (FYVE, RhoGEF and PH domain containing 2) - Rat Genome Database

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Gene: Fgd2 (FYVE, RhoGEF and PH domain containing 2) Rattus norvegicus
Analyze
Symbol: Fgd2
Name: FYVE, RhoGEF and PH domain containing 2
RGD ID: 1309840
Description: Predicted to have guanyl-nucleotide exchange factor activity and phosphatidylinositol phosphate binding activity. Predicted to be involved in cytoskeleton organization; filopodium assembly; and positive regulation of JUN kinase activity. Predicted to localize to early endosome; nucleus; and ruffle. Orthologous to human FGD2 (FYVE, RhoGEF and PH domain containing 2); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: FYVE, RhoGEF and PH domain-containing protein 2; LOC309653
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2207,424,795 - 7,441,603 (+)NCBI
Rnor_6.0 Ensembl206,973,398 - 6,990,023 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0206,973,356 - 6,990,026 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0209,212,072 - 9,228,719 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4207,684,764 - 7,702,116 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1207,685,169 - 7,701,720 (+)NCBI
Celera208,967,909 - 8,984,674 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,ISO)
cytoskeleton  (IEA)
early endosome  (ISO)
nucleus  (ISO)
ruffle  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:18838382  


Genomics

Comparative Map Data
Fgd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2207,424,795 - 7,441,603 (+)NCBI
Rnor_6.0 Ensembl206,973,398 - 6,990,023 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0206,973,356 - 6,990,026 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0209,212,072 - 9,228,719 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4207,684,764 - 7,702,116 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1207,685,169 - 7,701,720 (+)NCBI
Celera208,967,909 - 8,984,674 (+)NCBICelera
Cytogenetic Map20p12NCBI
FGD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl637,005,646 - 37,029,069 (+)EnsemblGRCh38hg38GRCh38
GRCh38637,005,655 - 37,029,072 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37636,973,431 - 36,996,845 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36637,081,401 - 37,104,822 (+)NCBINCBI36hg18NCBI36
Build 34637,081,400 - 37,104,822NCBI
Celera638,528,396 - 38,551,886 (+)NCBI
Cytogenetic Map6p21.2NCBI
HuRef636,691,770 - 36,715,184 (+)NCBIHuRef
CHM1_1636,975,223 - 36,998,669 (+)NCBICHM1_1
Fgd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391729,579,878 - 29,598,509 (+)NCBIGRCm39mm39
GRCm39 Ensembl1729,579,888 - 29,598,635 (+)Ensembl
GRCm381729,360,904 - 29,379,535 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1729,360,914 - 29,379,661 (+)EnsemblGRCm38mm10GRCm38
MGSCv371729,497,859 - 29,516,480 (+)NCBIGRCm37mm9NCBIm37
MGSCv361729,087,926 - 29,106,565 (+)NCBImm8
Celera1729,903,505 - 29,922,630 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1715.26NCBI
Fgd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554376,024,301 - 6,038,349 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554376,026,087 - 6,038,740 (-)NCBIChiLan1.0ChiLan1.0
FGD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1637,762,646 - 37,787,186 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl637,762,809 - 37,785,291 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0636,566,942 - 36,591,044 (+)NCBIMhudiblu_PPA_v0panPan3
FGD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1126,069,251 - 6,091,972 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl126,068,910 - 6,139,707 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha126,087,785 - 6,110,527 (+)NCBI
ROS_Cfam_1.0126,418,188 - 6,440,928 (+)NCBI
UMICH_Zoey_3.1126,072,861 - 6,095,355 (+)NCBI
UNSW_CanFamBas_1.0126,152,181 - 6,174,920 (+)NCBI
UU_Cfam_GSD_1.0126,250,596 - 6,273,316 (+)NCBI
Fgd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494641,513,954 - 41,536,375 (+)NCBI
SpeTri2.0NW_00493647622,423,851 - 22,442,795 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FGD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl732,648,222 - 32,674,537 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1732,648,260 - 32,674,539 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2737,551,703 - 37,577,990 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FGD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11735,112,453 - 35,136,161 (-)NCBI
ChlSab1.1 Ensembl1735,112,815 - 35,136,017 (-)Ensembl
Vero_WHO_p1.0NW_02366604436,943,781 - 36,967,321 (+)NCBI

Position Markers
AI411563  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2207,441,319 - 7,441,409 (+)MAPPER
Rnor_6.0206,989,740 - 6,989,829NCBIRnor6.0
Rnor_5.0209,228,433 - 9,228,522UniSTSRnor5.0
RGSC_v3.4207,701,833 - 7,701,922UniSTSRGSC3.4
Celera208,984,391 - 8,984,480UniSTS
RH 3.4 Map2078.24UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:260
Count of miRNA genes:176
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000041665
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 12 6 17 6 2 2
Low 1 43 45 35 2 35 8 11 74 35 39 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041665   ⟹   ENSRNOP00000039744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl206,973,398 - 6,990,023 (+)Ensembl
RefSeq Acc Id: NM_001107617   ⟹   NP_001101087
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,801 - 7,441,603 (+)NCBI
Rnor_6.0206,973,398 - 6,990,023 (+)NCBI
Rnor_5.0209,212,072 - 9,228,719 (+)NCBI
RGSC_v3.4207,684,764 - 7,702,116 (+)RGD
Celera208,967,909 - 8,984,674 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256205   ⟹   XP_006256267
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,799 - 7,441,552 (+)NCBI
Rnor_6.0206,973,357 - 6,990,026 (+)NCBI
Rnor_5.0209,212,072 - 9,228,719 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772729   ⟹   XP_008770951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0206,973,356 - 6,990,026 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601651   ⟹   XP_017457140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,430,582 - 7,441,552 (+)NCBI
Rnor_6.0206,979,232 - 6,990,026 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601652   ⟹   XP_017457141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0206,973,356 - 6,990,026 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098711   ⟹   XP_038954639
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,799 - 7,441,552 (+)NCBI
RefSeq Acc Id: XM_039098712   ⟹   XP_038954640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,799 - 7,441,552 (+)NCBI
RefSeq Acc Id: XM_039098713   ⟹   XP_038954641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,798 - 7,440,221 (+)NCBI
RefSeq Acc Id: XM_039098714   ⟹   XP_038954642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,796 - 7,436,470 (+)NCBI
RefSeq Acc Id: XM_039098715   ⟹   XP_038954643
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2207,424,795 - 7,431,876 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101087   ⟸   NM_001107617
- UniProtKB: D3Z9I3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256267   ⟸   XM_006256205
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008770951   ⟸   XM_008772729
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457141   ⟸   XM_017601652
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457140   ⟸   XM_017601651
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000039744   ⟸   ENSRNOT00000041665
RefSeq Acc Id: XP_038954643   ⟸   XM_039098715
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038954642   ⟸   XM_039098714
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038954641   ⟸   XM_039098713
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954639   ⟸   XM_039098711
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954640   ⟸   XM_039098712
- Peptide Label: isoform X2
Protein Domains
DH   FYVE-type   PH

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701446
Promoter ID:EPDNEW_R11970
Type:initiation region
Name:Fgd2_1
Description:FYVE, RhoGEF and PH domain containing 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0206,973,399 - 6,973,459EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309840 AgrOrtholog
Ensembl Genes ENSRNOG00000000528 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039744 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041665 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro DBL_dom_sf UniProtKB/TrEMBL
  DH-domain UniProtKB/TrEMBL
  FGD1-4_PH2 UniProtKB/TrEMBL
  FGD2_PH1 UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Znf_FYVE UniProtKB/TrEMBL
  Znf_FYVE-rel UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:309653 UniProtKB/TrEMBL
NCBI Gene 309653 ENTREZGENE
Pfam FYVE UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
PhenoGen Fgd2 PhenoGen
PROSITE DH_2 UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  ZF_FYVE UniProtKB/TrEMBL
SMART FYVE UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP DH-domain UniProtKB/TrEMBL
  FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt D3Z9I3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Fgd2  FYVE, RhoGEF and PH domain containing 2   Fgd2_predicted  FYVE, RhoGEF and PH domain containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Fgd2_predicted  FYVE, RhoGEF and PH domain containing 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED